
#######################################################
#                                                     #
#                        LGA                          #
#                  ---------------                    #
#                                                     #
#               Local-Global Alignment                #
#        A Method for Finding 3-D Similarities        #
#               in Protein Structures                 #
#                                                     #
#                  --------------- 06/2006            #
#                                                     #
#      Adam Zemla (adamz@llnl.gov)                    #
#      Lawrence Livermore National Laboratory, CA     #
#                                                     #
#######################################################

# Molecule1: number of CA atoms   23 (  113),  selected   23 , name T0347TS261_1_3-D1
# Molecule2: number of CA atoms   89 (  730),  selected   23 , name T0347_D1.pdb
# PARAMETERS: T0347TS261_1_3-D1.T0347_D1.pdb  -3  -ie  -o1  -sda  -d:4  
# FIXED Atom-Atom correspondence
# GDT and LCS analysis 

LCS - RMSD CUTOFF   5.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    16        93 - 108         2.22    27.76
  LCS_AVERAGE:     17.29

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    15        93 - 107         1.84    28.67
  LCS_AVERAGE:     12.70

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    13        94 - 106         0.60    29.76
  LCS_AVERAGE:     10.31

LCS_GDT    MOLECULE-1    MOLECULE-2    LENGTH_OF_THE
LCS_GDT     RESIDUE       RESIDUE         CONTINUOUS
LCS_GDT   NAME NUMBER   NAME NUMBER          SEGMENT     GLOBAL DISTANCE TEST - GDT_DATA_COLUMNS                             NUMBER OF THE RESIDUES:   89
LCS_GDT     A      23     A      23      3    3   14     0    3    3    3    3    5    5    6    7    7   10   10   10   11   11   13   14   14   14   19 
LCS_GDT     V      24     V      24      3    3   14     3    3    3    4    4    5    7    8    9    9   11   12   13   15   18   19   20   20   20   21 
LCS_GDT     G      25     G      25      4    5   14     4    6    6    6    6    7    8    9   10   13   15   16   17   17   18   19   20   20   20   21 
LCS_GDT     F      26     F      26      4    5   14     4    6    6    6    6    7    8    9   10   13   15   16   17   17   18   19   20   20   20   21 
LCS_GDT     R      27     R      27      4    5   14     4    6    6    6    6    7    8    9   10   13   15   16   17   17   18   19   20   20   20   21 
LCS_GDT     E      28     E      28      4    5   14     4    6    6    6    6    6    8    9    9   13   15   16   17   17   18   19   20   20   20   21 
LCS_GDT     V      29     V      29      4    5   14     0    3    4    5    5    6    7    8    9   10   11   16   17   17   18   19   20   20   20   21 
LCS_GDT     H      93     H      93     10   15   16     3    6   10   13   14   14   14   16   16   16   16   16   16   16   16   16   16   17   18   19 
LCS_GDT     L      94     L      94     13   15   16     5   10   13   13   14   14   14   16   16   16   16   16   16   16   16   19   20   20   20   21 
LCS_GDT     G      95     G      95     13   15   16     7   12   13   13   14   14   14   16   16   16   16   16   17   17   18   19   20   20   20   21 
LCS_GDT     K      96     K      96     13   15   16    11   12   13   13   14   14   14   16   16   16   16   16   17   17   18   19   20   20   20   21 
LCS_GDT     D      97     D      97     13   15   16    11   12   13   13   14   14   14   16   16   16   16   16   17   17   18   19   20   20   20   21 
LCS_GDT     E      98     E      98     13   15   16    11   12   13   13   14   14   14   16   16   16   16   16   17   17   18   19   20   20   20   21 
LCS_GDT     F      99     F      99     13   15   16    11   12   13   13   14   14   14   16   16   16   16   16   17   17   18   19   20   20   20   21 
LCS_GDT     W     100     W     100     13   15   16    11   12   13   13   14   14   14   16   16   16   16   16   17   17   18   19   20   20   20   21 
LCS_GDT     S     101     S     101     13   15   16    11   12   13   13   14   14   14   16   16   16   16   16   17   17   18   19   20   20   20   21 
LCS_GDT     V     102     V     102     13   15   16    11   12   13   13   14   14   14   16   16   16   16   16   17   17   18   19   20   20   20   21 
LCS_GDT     M     103     M     103     13   15   16    11   12   13   13   14   14   14   16   16   16   16   16   17   17   18   19   20   20   20   21 
LCS_GDT     D     104     D     104     13   15   16    11   12   13   13   14   14   14   16   16   16   16   16   16   17   18   19   20   20   20   21 
LCS_GDT     H     105     H     105     13   15   16    11   12   13   13   14   14   14   16   16   16   16   16   17   17   18   19   20   20   20   21 
LCS_GDT     R     106     R     106     13   15   16    11   12   13   13   14   14   14   16   16   16   16   16   17   17   18   19   20   20   20   21 
LCS_GDT     N     107     N     107      3   15   16     3    3    3    4    5    7   13   16   16   16   16   16   17   17   18   19   20   20   20   21 
LCS_GDT     L     108     L     108      3    4   16     3    3    3    4    4    9   13   16   16   16   16   16   16   16   16   18   19   20   20   21 
LCS_AVERAGE  LCS_A:  13.43  (  10.31   12.70   17.29 )

GLOBAL_DISTANCE_TEST (the largest set of residues that can fit under specified DISTANCE_CUTOFF)
GDT DIST_CUTOFF  0.50   1.00   1.50   2.00   2.50   3.00   3.50   4.00   4.50   5.00   5.50   6.00   6.50   7.00   7.50   8.00   8.50   9.00   9.50  10.00
GDT NUMBER_CA     11     12     13     13     14     14     14     16     16     16     16     16     17     17     18     19     20     20     20     21 
GDT PERCENT_CA  12.36  13.48  14.61  14.61  15.73  15.73  15.73  17.98  17.98  17.98  17.98  17.98  19.10  19.10  20.22  21.35  22.47  22.47  22.47  23.60
GDT RMS_LOCAL    0.24   0.37   0.60   0.60   1.08   1.08   1.08   2.22   2.22   2.22   2.22   2.22   4.57   4.57   4.78   5.04   5.55   5.36   5.36   5.84
GDT RMS_ALL_CA  29.82  29.83  29.76  29.76  29.49  29.49  29.49  27.76  27.76  27.76  27.76  27.76   7.42   7.42   7.49   7.44   7.19   7.50   7.50   7.23

#      Molecule1      Molecule2       DISTANCE
LGA    A      23      A      23         48.038
LGA    V      24      V      24         46.566
LGA    G      25      G      25         46.842
LGA    F      26      F      26         52.234
LGA    R      27      R      27         55.057
LGA    E      28      E      28         48.794
LGA    V      29      V      29         45.590
LGA    H      93      H      93          1.744
LGA    L      94      L      94          2.101
LGA    G      95      G      95          1.399
LGA    K      96      K      96          0.915
LGA    D      97      D      97          2.329
LGA    E      98      E      98          2.234
LGA    F      99      F      99          1.224
LGA    W     100      W     100          1.595
LGA    S     101      S     101          1.316
LGA    V     102      V     102          1.894
LGA    M     103      M     103          2.874
LGA    D     104      D     104          2.394
LGA    H     105      H     105          0.998
LGA    R     106      R     106          3.314
LGA    N     107      N     107          3.965
LGA    L     108      L     108          3.805

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   23   89    4.0     16    2.22    16.854    15.693     0.689

LGA_LOCAL      RMSD =  2.221  Number of atoms =   16  DIST =   4.00
LGA_ALL_ATOMS  RMSD = 27.167  Number of atoms =   23 
Std_ALL_ATOMS  RMSD =  7.048  (standard rmsd on all 23 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.349831 * X  +  -0.685701 * Y  +   0.638304 * Z  +  16.278080
  Y_new =   0.840871 * X  +  -0.530204 * Y  +  -0.108723 * Z  +  12.406295
  Z_new =   0.412983 * X  +   0.498696 * Y  +   0.762068 * Z  + -54.887451 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   0.579461   -2.562131  [ DEG:    33.2007   -146.7993 ]
  Theta =  -0.425727   -2.715866  [ DEG:   -24.3923   -155.6077 ]
  Phi   =   1.965049   -1.176544  [ DEG:   112.5890    -67.4110 ]
 
# END of job
REMARK  ---------------------------------------------------------- 
REMARK   Citing LGA: 
REMARK   Zemla A., LGA - a Method for Finding 3D Similarities in  
REMARK   Protein Structures, Nucleic Acids Research, 2003, V. 31, 
REMARK   No. 13, pp. 3370-3374. 
REMARK  ---------------------------------------------------------- 
REMARK   Superimposed MOLECULES (1=>2)   Output: 1 molecule      
REMARK     1: T0347TS261_1_3-D1                             
REMARK     2: T0347_D1.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0347TS261_1_3-D1.T0347_D1.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   23   89   4.0   16   2.22  15.693     7.05
REMARK  ---------------------------------------------------------- 
MOLECULE T0347TS261_1_3-D1
REMARK PARENT number 3
PFRMAT TS
TARGET T0347
PARENT 2gok_A
ATOM    786  N   ALA    23      17.144   8.531  18.669  1.00  4.96
ATOM    787  CA  ALA    23      18.540   8.102  18.701  1.00  4.96
ATOM    788  C   ALA    23      19.299   8.655  17.505  1.00  4.96
ATOM    789  O   ALA    23      20.486   8.949  17.602  1.00  4.96
ATOM    790  CB  ALA    23      18.657   6.569  18.681  1.00  4.96
ATOM    791  N   VAL    24      18.616   8.777  16.371  1.00  4.37
ATOM    792  CA  VAL    24      19.255   9.320  15.181  1.00  4.37
ATOM    793  C   VAL    24      19.659  10.772  15.460  1.00  4.37
ATOM    794  O   VAL    24      20.775  11.197  15.150  1.00  4.37
ATOM    795  CB  VAL    24      18.295   9.268  13.993  1.00  4.37
ATOM    796  N   GLY    25      18.748  11.535  16.050  1.00  1.00
ATOM    797  CA  GLY    25      19.041  12.926  16.369  1.00  1.00
ATOM    798  C   GLY    25      20.184  12.974  17.384  1.00  1.00
ATOM    799  O   GLY    25      21.120  13.757  17.252  1.00  1.00
ATOM    800  N   PHE    26      20.115  12.103  18.382  1.00  4.60
ATOM    801  CA  PHE    26      21.134  12.028  19.424  1.00  4.60
ATOM    802  C   PHE    26      22.516  11.622  18.917  1.00  4.60
ATOM    803  O   PHE    26      23.528  12.198  19.318  1.00  4.60
ATOM    804  CB  PHE    26      20.727  10.998  20.509  1.00  4.60
ATOM    805  N   ARG    27      22.551  10.624  18.036  1.00  5.20
ATOM    806  CA  ARG    27      23.812  10.082  17.527  1.00  5.20
ATOM    807  C   ARG    27      24.406  10.711  16.281  1.00  5.20
ATOM    808  O   ARG    27      25.631  10.779  16.143  1.00  5.20
ATOM    809  CB  ARG    27      23.676   8.578  17.251  1.00  5.20
ATOM    810  N   GLU    28      23.552  11.144  15.363  1.00  4.42
ATOM    811  CA  GLU    28      24.043  11.717  14.117  1.00  4.42
ATOM    812  C   GLU    28      23.792  13.210  13.948  1.00  4.42
ATOM    813  O   GLU    28      24.729  13.985  13.737  1.00  4.42
ATOM    814  CB  GLU    28      23.427  10.981  12.902  1.00  4.42
ATOM    815  N   VAL    29      22.533  13.614  14.043  1.00  4.33
ATOM    816  CA  VAL    29      22.195  15.012  13.834  1.00  4.33
ATOM    817  C   VAL    29      22.908  15.991  14.757  1.00  4.33
ATOM    818  O   VAL    29      23.603  16.895  14.277  1.00  4.33
ATOM    819  CB  VAL    29      20.672  15.245  13.918  1.00  4.33
ATOM    820  N   HIS    93       0.338  22.370   2.332  1.00  2.37
ATOM    821  CA  HIS    93      -0.739  22.248   3.316  1.00  2.37
ATOM    822  C   HIS    93      -0.757  23.317   4.408  1.00  2.37
ATOM    823  O   HIS    93      -1.363  23.130   5.464  1.00  2.37
ATOM    824  CB  HIS    93      -0.686  20.854   3.961  1.00  2.37
ATOM    825  N   LEU    94      -0.092  24.436   4.160  1.00  4.16
ATOM    826  CA  LEU    94      -0.061  25.515   5.136  1.00  4.16
ATOM    827  C   LEU    94      -1.462  26.122   5.292  1.00  4.16
ATOM    828  O   LEU    94      -2.123  26.414   4.295  1.00  4.16
ATOM    829  CB  LEU    94       0.917  26.598   4.677  1.00  4.16
ATOM    830  N   GLY    95      -1.910  26.311   6.532  1.00  5.18
ATOM    831  CA  GLY    95      -3.220  26.909   6.776  1.00  5.18
ATOM    832  C   GLY    95      -3.076  28.410   7.021  1.00  5.18
ATOM    833  O   GLY    95      -1.960  28.931   7.058  1.00  5.18
ATOM    834  N   LYS    96      -4.203  29.099   7.187  1.00  4.51
ATOM    835  CA  LYS    96      -4.199  30.543   7.407  1.00  4.51
ATOM    836  C   LYS    96      -3.392  30.978   8.625  1.00  4.51
ATOM    837  O   LYS    96      -2.676  31.982   8.578  1.00  4.51
ATOM    838  CB  LYS    96      -5.633  31.062   7.547  1.00  4.51
ATOM    839  N   ASP    97      -3.521  30.228   9.717  1.00  4.54
ATOM    840  CA  ASP    97      -2.802  30.534  10.946  1.00  4.54
ATOM    841  C   ASP    97      -1.305  30.463  10.673  1.00  4.54
ATOM    842  O   ASP    97      -0.534  31.305  11.138  1.00  4.54
ATOM    843  CB  ASP    97      -3.162  29.532  12.065  1.00  4.54
ATOM    844  N   GLU    98      -0.907  29.449   9.908  1.00  5.12
ATOM    845  CA  GLU    98       0.490  29.272   9.571  1.00  5.12
ATOM    846  C   GLU    98       1.026  30.427   8.749  1.00  5.12
ATOM    847  O   GLU    98       2.119  30.917   9.020  1.00  5.12
ATOM    848  CB  GLU    98       0.658  27.938   8.823  1.00  5.12
ATOM    849  N   PHE    99       0.263  30.862   7.750  1.00  6.45
ATOM    850  CA  PHE    99       0.677  31.970   6.896  1.00  6.45
ATOM    851  C   PHE    99       0.938  33.236   7.709  1.00  6.45
ATOM    852  O   PHE    99       1.919  33.945   7.477  1.00  6.45
ATOM    853  CB  PHE    99      -0.382  32.240   5.840  1.00  6.45
ATOM    854  N   TRP   100       0.053  33.516   8.660  1.00  3.02
ATOM    855  CA  TRP   100       0.188  34.691   9.517  1.00  3.02
ATOM    856  C   TRP   100       1.407  34.572  10.432  1.00  3.02
ATOM    857  O   TRP   100       2.083  35.565  10.701  1.00  3.02
ATOM    858  CB  TRP   100      -1.081  34.875  10.359  1.00  3.02
ATOM    859  N   SER   101       1.691  33.363  10.903  1.00  4.62
ATOM    860  CA  SER   101       2.836  33.145  11.777  1.00  4.62
ATOM    861  C   SER   101       4.127  33.436  11.017  1.00  4.62
ATOM    862  O   SER   101       5.053  34.037  11.555  1.00  4.62
ATOM    863  CB  SER   101       2.844  31.713  12.293  1.00  4.62
ATOM    864  N   VAL   102       4.181  33.016   9.757  1.00  5.57
ATOM    865  CA  VAL   102       5.365  33.248   8.944  1.00  5.57
ATOM    866  C   VAL   102       5.586  34.741   8.701  1.00  5.57
ATOM    867  O   VAL   102       6.695  35.241   8.866  1.00  5.57
ATOM    868  CB  VAL   102       5.254  32.506   7.604  1.00  5.57
ATOM    869  N   MET   103       4.530  35.450   8.314  1.00  6.50
ATOM    870  CA  MET   103       4.636  36.883   8.056  1.00  6.50
ATOM    871  C   MET   103       5.038  37.630   9.327  1.00  6.50
ATOM    872  O   MET   103       5.878  38.529   9.298  1.00  6.50
ATOM    873  CB  MET   103       3.311  37.418   7.531  1.00  6.50
ATOM    874  N   ASP   104       4.431  37.255  10.445  1.00  2.99
ATOM    875  CA  ASP   104       4.724  37.898  11.722  1.00  2.99
ATOM    876  C   ASP   104       6.189  37.711  12.129  1.00  2.99
ATOM    877  O   ASP   104       6.812  38.626  12.666  1.00  2.99
ATOM    878  CB  ASP   104       3.797  37.332  12.807  1.00  2.99
ATOM    879  N   HIS   105       6.732  36.524  11.864  1.00  3.56
ATOM    880  CA  HIS   105       8.113  36.214  12.213  1.00  3.56
ATOM    881  C   HIS   105       9.109  36.758  11.196  1.00  3.56
ATOM    882  O   HIS   105      10.292  36.890  11.496  1.00  3.56
ATOM    883  CB  HIS   105       8.289  34.694  12.342  1.00  3.56
ATOM    884  N   ARG   106       8.630  37.058   9.994  1.00  5.11
ATOM    885  CA  ARG   106       9.513  37.557   8.954  1.00  5.11
ATOM    886  C   ARG   106      10.152  36.409   8.194  1.00  5.11
ATOM    887  O   ARG   106      11.132  36.593   7.478  1.00  5.11
ATOM    888  CB  ARG   106      10.579  38.469   9.584  1.00  5.11
ATOM    889  N   ASN   107       9.595  35.213   8.357  1.00  4.78
ATOM    890  CA  ASN   107      10.106  34.024   7.683  1.00  4.78
ATOM    891  C   ASN   107       9.617  34.013   6.234  1.00  4.78
ATOM    892  O   ASN   107       8.425  34.185   5.976  1.00  4.78
ATOM    893  CB  ASN   107       9.619  32.738   8.401  1.00  4.78
ATOM    894  N   LEU   108      10.533  33.826   5.287  1.00  6.09
ATOM    895  CA  LEU   108      10.157  33.796   3.879  1.00  6.09
ATOM    896  C   LEU   108       9.487  32.471   3.525  1.00  6.09
ATOM    897  O   LEU   108       9.908  31.411   3.979  1.00  6.09
ATOM    898  CB  LEU   108      11.385  33.972   2.959  1.00  6.09
TER
END
